If I buy one of these tickets, it says that I can also use the train before or after, without changing the booking.

Does this still apply even if the route and / or the semi-flexible fare is different to one booked?

Your pre booked seat wont be valid but you can travel on service before/after provided the routeing is available in the JP and yes even if there is a fare difference (not common). They do however have a clause saying subject to availability, so at busy times they can refuse such travel but its unlikely.